MLSTar: automatic multilocus sequence typing of bacterial genomes in R

Area of Science:

• * Computational Biology
• * Bioinformatics
• * Microbial Genomics

Background:

• * Multilocus sequence typing (MLST) is a standard method for assessing genetic variation in bacterial populations and epidemiology.
• * Traditional MLST relies on analyzing a limited number of housekeeping genes, assigning arbitrary integer identifiers to alleles.
• * The advent of whole-genome sequencing enables the extension of MLST by automating allele information extraction from extensive genomic data.

Purpose of the Study:

• * To introduce MLSTar, the first R package designed for automated MLST analysis using whole-genome sequences.
• * To facilitate seamless integration with the PubMLST database for scheme selection and allele assignment.
• * To enable efficient data analysis and visualization of MLST data within the R environment.

Main Methods:

• * Development of MLSTar as an R package for automated allele and sequence type assignment from bacterial genomes.
• * Integration with the PubMLST database to access a wide array of MLST schemes.
• * Application of MLSTar to analyze over 2,500 bacterial genomes across diverse species.

Main Results:

• * MLSTar accurately assigns alleles and sequence types from whole-genome sequences.
• * The package demonstrates comparable performance to existing command-line tools for MLST analysis.
• * Successful application across multiple bacterial species, validating its broad utility.

Conclusions:

• * MLSTar provides a powerful and accurate tool for automated MLST analysis in R.
• * It simplifies the process of leveraging whole-genome sequencing data for bacterial population studies.
• * The package enhances microbial genomics research by enabling efficient data analysis and visualization.